Although performing scans with your spaceship in-game adds to the Sporepedia, it doesn't keep track of where you've seen a particular creature. So, if you care, say because you want to use a particular species for terraforming, you either have to keep track yourself or go find it again planet-by-planet. The Sporepedia acts like it's mostly out-of-game.
You can create a Sporecast of favorite creations and subscribe to other people's to automatically download their content. But putting together a Sporecast is a giant pain. You can create one from the web page but not update its content there. You can't drag-and-drop from the other sections of the Sporepedia, you can only perform searches on the online database. So even simple things like adding a building you just made, or an animal you encountered in-game, are difficult. And, when I do a search, some of my own more-recent creations are missing. (I would guess they're not present in the search index yet because they do show up in the "my creations" web page.)
And did I mention that the online interactions are slow?
And the web page layout is screwed up, so that the advertisement often covers some content.
I'm glad that they finally released the game (I'm having fun playing it) but this feature seems half-baked.